CRISPR · Software
MAGeCK
Identifies functionally important genes from genome-scale CRISPR-Cas9 knockout screens using sgRNA read counts.
What MAGeCK is
Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a bioinformatics software tool designed to identify critical genes from genome-scale CRISPR-Cas9 knockout screening data. It was developed by Wei Li and Han Xu in Xiaole Shirley Liu's laboratory at the Dana-Farber Cancer Institute and the Harvard School of Public Health, and is maintained by the Wei Li laboratory at Children's National Medical Center.
The software addresses the challenge of statistically evaluating sgRNA abundance across experimental conditions. By processing sgRNA read counts through a dedicated screening pipeline, MAGeCK enables researchers to detect significant knockout effects with high sensitivity and a low false discovery rate, while producing publication-standard graphical visualisations.
How it works
MAGeCK takes sgRNA read count tables derived from CRISPR-Cas9 knockout screens as input. Built using C and Python, it executes statistical analysis across the screen data to evaluate sgRNA performance and rank target genes according to their significance.
Key facts
- Maintainer
- Wei Li laboratory (Children's National Medical Center)
- Software version
- 0.5.9.5
- Implementation languages
- C, Python
- Primary input
- sgRNA read counts
- Intended application
- CRISPR-Cas9 knockout screen analysis
What you can use it for
- Genome-wide knockout screen analysis
- Identifying essential or phenotype-associated genes across genome-scale CRISPR-Cas9 knockout studies.
- sgRNA count evaluation
- Assessing sgRNA abundance and statistical enrichment or depletion from raw sequence read count tables.
- Screen result visualisation
- Generating publication-standard diagnostic and summary figures representing screen outcomes.
Run it here
MAGeCK is preinstalled on the machine behind every research conversation. Ask the agent in plain language, or give it the exact command — it runs it, reads the output and explains it.
Try asking
“Find the essential genes in this CRISPR screen count table with MAGeCK.”
Strengths and limits
Good at
- Delivers high sensitivity while maintaining a low false discovery rate during screening analysis.
- Includes built-in visualisation utilities to generate publication-standard figures.
- Provides a straightforward pipeline supported by documentation and introductory tutorials.
Questions
Can I run MAGeCK online without installing it?
MAGeCK is preinstalled on the machine behind every research conversation. Ask the agent in plain language, or give it the exact command — it runs it, reads the output and explains it.
What licence is MAGeCK under?
MAGeCK is published under its authors' own licence; the project page at https://sourceforge.net/projects/mageck/ states it.
What input data does MAGeCK require?
MAGeCK requires sgRNA read count data generated from CRISPR-Cas9 knockout screening experiments.
What programming languages are used in MAGeCK?
The tool is implemented in C and Python.
What outputs does MAGeCK generate?
It identifies significant candidate genes from knockout screens and produces publication-standard visualisation plots.
Written from MAGeCK's own README and project page. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.